[gmx-users] COM pulling - speptide

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 25 12:54:19 CEST 2010

C Johnson wrote:
>>If you're proceeding blindly, then you're likely going to frustrate yourself to 
>>no end.  There is literature relevant to what you're doing - pulling on 
>>peptides/proteins to unfold them is something that's been done.  So you should 
>>have some methodological precedent.
>>"Non-Protein" is a default group that should have been written to the .ndx file 
>>by make_ndx.  The only reason I can see for this error to come up is if you've 
>>removed it from the pull.ndx file.  If you're using my .mdp file, then 
>>Non-Protein is a temperature coupling group.
> I know there is literature relevant but is there any that explains how to do it in Gromacs?  

I don't know.  All I implied was that some of the mystery can be taken out of 
the process.  A good Methods section can be translated to the parameters needed 
by Gromacs as input.  Usually "how-to" material is reserved for tutorials, not 
the literature.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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